Note: violent chapter ahead! If you've read this far, I'm going to assume that you've played or at least seen footage of the battles at the end of the game. This story isn't really about them, so that's why I didn't go into extensive detail.
Destroying the barriers protecting Ganondorf's keep was little effort for Link, his anger fueling his drive forward. He raced up the steps of the inner tower, slicing down several lizalfos and iron knuckles. When he thought he had reached the top, he found only a locked door.
"The key's over here."
Link took his time turning around, knowing exactly who it was that taunted him. Sure enough, Agahnim was leaning against the opposite wall, twirling the key around his finger.
"You took my Princess's purity. We had hoped to have the shadow demon do it, after all physical pain would have made the mental pain all that more real. But I guess I should give you some credit, after all you lasted a lot longer than the average virile male would. I wonder if her silly insistence that she's not female had anything to do with that?"
The hero growled, grabbing a torch from a nearby sconce and whipping it at the mage.
"Oh no, boy, I'm not falling for the same trick twice," Agahnim quipped as he ducked the torch. He lashed out with a wave of dark magic, which Link sliced back with his sword. But instead of returning like in the battle with Phantom Ganon, the wave split into six fragments and two hit Link in the stomach.
Link shook it off and lunged at the mage, finding that his sword strikes phased right through him.
"Heh, what's wrong, never seen duplication magic before?" Link did not have time to react before he was hit in the back of the head, the Agahnim in front of him dissolving. The real Agahnim stepped out from behind, brandishing a flail. He smacked Link again, causing the hero to collapse onto the floor unconscious.
"What a stupid kid," Agahnim growled, before dragging Link by his leg into the main room where his master was waiting. "Master, your guest has arrived!" High above the organ in front of the evil king, Zelda watched from her imprisonment as the mage tossed the hero to the floor. Suddenly her right hand lit up with the glow of the Triforce of Wisdom. Link's immobile hand lit up as well, causing Ganondorf to stop playing.
"The Triforce parts are resonating... They are combining into one again... The two Triforce parts that I could not capture on that day seven years ago... I did not expect they would be hidden within you two! And now, finally, all the Triforce parts have gathered here. These toys are too much for you! I command you to return them to me!"
Agahnim grinned as his master approached the unconscious hero, and moved to the side to get a better view. Suddenly Link sprang up from his feint, gripping the Master Sword and slashing it across Agahnim's chest.
"Guahh!" Agahnim screamed as he fell backward, giving Link an opening to thrust the sword through his ribs.
'For what you did to Navi!' Link hissed, and kicked the slain mage from his blade.
"Heh heh heh, the Hero of Time has finally learned how to use his surroundings in battle," Ganondorf mused as he regarded his fallen captain. "You've taken my Sheikah from me, boy. I guess then that it is only fair I do the same." He moved from in front of the organ bench with a flourish of his cape, and kicked it forward. When it hit the ground, a body fell out from it.
'SHEIK!'
Ganondorf used a wave of dark magic to keep Link at bay as he knelt over the unconscious and bleeding guide. "Your woman is weak, hero. Normally, cornered mice will attempt to bite the cat who trapped them. But in her case, she chose to insult me instead of fight." He wrapped his hand around their neck and jaw, squeezing until Link could hear the jawbones cracking.
'STOP IT! LEAVE THEM ALONE!'
"Oh no, boy. She brought this upon herself. Too bad she lacks the curves of a woman, her face was quite lovely..." Ganondorf used his fingernails to scratch at Sheik's cheek, then turned his attention to her stomach. "Perhaps we should have her awake for this, after all she'll want to see how much pain is on your face..."
'GODDESSES, NO!' Link panicked and Zelda screamed, but neither could keep Ganondorf from returning Sheik to consciousness. Sheik's eyes darted open, immediately grimacing from the broken jaw.
"Look, little Sheikah, your knight in shining armor has come to watch you die."
Sheik's eyes widened, and they frantically scanned the room as best they could without moving. Out of the corner of their eye they could see Link trembling. Without warning Ganondorf dragged his nails across their stomach, slicing through their clothing and leaving large gashes across their midsection. He grabbed their neck again, this time hoisting them up into the air and holding a knife to their throat.
"Say goodbye to your hero, Sheikah."
A sudden spark of energy broke out from across the room, and Ganondorf turned in time to see an arrow headed his way. He threw Sheik to the side and dodged it, before another one hit his leg. Link had managed to break the evil king's barrier with Zelda's Light Arrows, and while Ganondorf seethed, he rushed to the fallen Sheikah's side.
'Sheik...' Tears slid down Link's face as he held Sheik to his chest. 'Please... hang on...'
Sheik managed to grip Link's hand as their life faded from them, and used the contact to send him a message. Link... hurry... kill that monster and save Hyrule. If not for the Princess, then for Navi...
'No, Sheik! Stay with me! SHEIK!' Sheik's arm fell from Link's hand, and Link screamed through his tears. 'Hang on, love... hang on...'
Link stood, rage clouding his vision. He lunged at Ganondorf, just as the evil king finished shaking off the Light Arrow's magic. Link sliced back the bolt of magic Ganondorf threw at him, then fired another Light Arrow. This time Link was close enough to strike, and drove the Master Sword through the evil king's chest.
"GRAHHH!" Ganondorf recoiled in pain, but managed to catch Link's shoulder with his knife. Link jumped back, reflecting another magical blast.
"You rotten kid, you think you will be able to beat me using my own magic? Burn in hell!" The evil king started summoning a large orb of energy above his head to throw at Link, but Link was smarter and used the distraction to fire a Light Arrow into Ganondorf's chest wound. It caused him to lose focus and fall to the ground, where Link was waiting with a spin attack.
It connected, causing Ganondorf to stagger and collapse. "The Great Evil King Ganondorf... beaten by this kid?!" He vomited blood before reaching out to Link. "If I die, you and your women die with me!"
The entire tower started shaking, causing Zelda's crystalline prison to fall to the floor and shatter, setting her free. "Link, listen to me! This tower will collapse soon! With his last breath, Ganondorf is trying to crush us in the ruins of the tower! We need to hurry and escape! Over here!" Zelda ran over to a set of bars on the wall, which disappeared once exposed to her magic. She turned expecting to find Link behind her, but instead he was fetching Sheik.
"Come ON! We don't have much time!" Zelda recoiled in horror at the dirty look Link gave her for suggesting that he leave Sheik, and instead ran ahead to open the other gates.
Link cradled Sheik to his chest as he followed the Princess. 'It's okay, I'll get you out. Just hang on...' He ducked and dodged the falling debris, and made it out of the tower with Zelda just as it collapsed.
Ganondorf's body lay in a pile of rubble at the center of the foundation. Zelda quickly called upon the Sages to seal him before he recovered. "Ancient Creators of Hyrule! Now, open the sealed door and send the Evil Incarnation of Darkness into the void of the Evil Realm!"
The evil king cursed as the Sages portal swallowed him up into the confines of the Sacred Realm. When it was over, Zelda turned to Link. "Thank you, Link. Thanks to you, Ganondorf has been sealed inside the Evil Realm! Thus, peace will once again reign in this world..."
But Link was not paying attention. He had already started towards the Great Fairy of Courage's fountain, his battered and broken love in his arms. Peace may once again come to Hyrule, but he had no cause to look forward to it as the one person he fought for was dying.
